My family has owned 2 Subaru Outbacks that have been used for towing various boats, and our experiences have been... mixed. Some of this is not the car's fault, but still wasn't a good thing.
First one was a '98 2.0L (or closest, this is from my memory and I was 6 at the time) 5 speed manual, which we towed two boats with. First one (3 metre boat, not too many fancy bits so it would have been fairly light) was a breeze, it could handle it (I daresay this would be the most relevant example for you). Second boat was a 4.75m Quintrex Bayhunter Caprice, with as 75 hp Yamaha, canopy, the works. We blew the clutch up on that one, so we sold it and got our second (and current) Outback
This one is an '02 H6 3.0L Luxury with a 4 speed auto (they didn't do manuals in this one due to "a lack of space for the manual gearbox"). This will tow almost anything with no troubles, artially due to the auto-box (but mostly due to the engine that just seems to be made for it). Downsides? It guzzles fuel as if it was going out of fashion (something like 11L per 100km or similar) and you can't turn AWD off (ala Suzuki SX4- this helps add to the fuel problem). We are currently in the process of selling ours now as it is too big for us (rarely have 4 people in it and we don't need as big a car to tow our new smaller boat) and small niggles (eg CV boots/joints or whatever they are called) are costing us a ton in repairs.
Now, the main reason why the clutch on our first Scooby was because of a factor not many peopletake into account (it was one we sure as hell didn't!)- the "conditions" (for want of a better term) that the towing will occur in. Moving our boat into and out of its carport is a nightmare- it's a cramped little concrete slab on the side of our house, and you have to reverse it up a not too steep (but still significant) grass hill to get it in there. Now this may have partially been my dad's skill level (but I doubt it, he's pretty damn good), but the clutch just couldn't handle that sort of reversing and parking- the constant clutch in/out and holding at friction point to make sure we didn't crash the boat into the side of our house/the fence just killed it. Even an empty trailer would cause us to start to smell the burning. So if getting the jet ski in/out of where it is stored is problematic and harsh on the car/clutch in any way, a manual may not be the best option. But that's just my experience, and usual towing of a load within the limits of the car won't do that to a manual IMO.
Subarus from that era are nice cars though, we were really sad to let go of our 98 one and we still see it being driven around by the current owner today (and feel a pang of sorrow!)